Aqueous two-phase extraction (ATPE) of R-Phycoerythrin (R-PE), a fluorescent and commercially valuable protein, was carried out in two parallel schemes. In scheme-1, ATPE alone was employed, and in scheme-2, process-integration was attempted, where primary extract was subjected to precipitation before standardization of process parameters of ATPE. Scheme-1 with polyethylene glycol (PEG)-3350/potassium phosphate system has resulted in very low R-PE yield (26% w/w) without much enrichment in purity (0.3). In scheme-2, PEG-1450/ potassium phosphate system (pH 6, fie-line length 12.26% and lower volume-ratio) has resulted in higher R-PE purity (0.74) with 72% yield. R-PE containing PEG-rich (top) phase was subjected to ultrafiltration, to remove phase forming components, resulting in further increase in R-PE purity (1.1). Overall enrichment in R-PE purity of 11-fold with 57% (w/w) yield and removal of about 95% of total sugars was achieved in scheme-2. Intactness of R-PE after processing was confirmed by absorbance and emission spectrum analysis.